Sex chromosome positions in human interphase nuclei as studied by in situ hybridization with chromosome specific DNA probes

Two cloned repetitive DNA probes, pXBR and CY1, which bind preferentially to specific regions of the human X and Y chromosome, respectively, were used to study the distribution of the sex chromosomes in human lymphocyte nuclei by in situ hybridization experiments. Our data indicate a large variability of the distances between the sex chromosomes in male and female interphase nuclei. However, the mean distance observed between the X and Y chromosome was significantly smaller than the mean distance observed between the two X-chromosomes. The distribution of distances determined experimentally is compared with three model distributions of distances, and the question of a non-random distribution of sex chromosomes is discussed. Mathematical details of these model distributions are provided in an Appendix to this paper. In the case of a human translocation chromosome (XqterXp22.2::Yq11Y qter) contained in the Chinese hamster x human hybrid cell line 445 x 393, the binding sites of pXBR and CY1 were found close to each other in most interphase nuclei. These data demonstrate the potential use of chromosome-specific repetitive DNA probes to study the problem of interphase chromosome topography

Detection of chromosome aberrations in the human interphase nucleus by visualization of specific target DNAs with radioactive and non-radioactive in situ hybridization techniques: diagnosis of trisomy 18 with probe L1.84

The localization of chromosome 18 in human interphase nuclei is demonstrated by use of radioactive and nonradioactive in situ hybridization techniques with a DNA clone designated L1.84. This clone represents a distinct subpopulation of the repetitive human alphoid DNA family, located in the centric region of chromosome 18. Under stringent hybridization conditions hybridization of L1.84 is restricted to chromosome 18 and reflects the number of these chromosomes present in the nuclei, namely, two in normal diploid human cells and three in nuclei from cells with trisomy 18. Under conditions of low stringency, cross-hybridization with other subpopulations of the alphoid DNA family occurs in the centromeric regions of the whole chromosome complement, and numerous hybridization sites are detected over interphase nuclei. Detection of chromosome-specific target DNAs by non-radioactive in situ hybridization with appropriate DNA probes cloned from individual chromosomal subregions presents a rapid means of identifying directly numerical or even structural chromosome aberrations in the interphase nucleus. Present limitations and future applications of interphase cytogenetics are discussed

Prezygotic Barriers to Hybridization in Marine Broadcast Spawners: Reproductive Timing and Mating System Variation

Sympatric assemblages of congeners with incomplete reproductive barriers offer the opportunity to study the roles that ecological and non-ecological factors play in reproductive isolation. While interspecific asynchrony in gamete release and gametic incompatibility are known prezygotic barriers to hybridization, the role of mating system variation has been emphasized in plants. Reproductive isolation between the sibling brown algal species Fucus spiralis, Fucus guiryi (selfing hermaphrodite) and Fucus vesiculosus (dioecious) was studied because they form hybrids in parapatry in the rocky intertidal zone, maintain species integrity over a broad geographic range, and have contrasting mating systems. We compared reproductive synchrony (spawning overlap) between the three species at several temporal scales (yearly/seasonal, semilunar/tidal, and hourly during single tides). Interspecific patterns of egg release were coincident at seasonal (single peak in spring to early summer) to semilunar timescales. Synthesis of available data indicated that spawning is controlled by semidiurnal tidal and daily light-dark cues, and not directly by semilunar cycles. Importantly, interspecific shifts in timing detected at the hourly scale during single tides were consistent with a partial ecological prezygotic hybridization barrier. The species displayed patterns of gamete release consistent with a power law distribution, indicating a high degree of reproductive synchrony, while the hypothesis of weaker selective constraints for synchrony in selfing versus outcrossing species was supported by observed spawning in hermaphrodites over a broader range of tidal phase than in outcrossers. Synchronous gamete release is critical to the success of external fertilization, while high-energy intertidal environments may offer only limited windows of reproductive opportunity. Within these windows, however, subtle variations in reproductive timing have evolved with the potential to form ecological barriers to hybridization

Testing statistical significance scores of sequence comparison methods with structure similarity

BACKGROUND: In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. RESULTS: All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. CONCLUSION: The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons

Study protocol: a randomised controlled trial investigating the effect of exercise training on peripheral blood gene expression in patients with stable angina

Background: Exercise training has been shown to reduce angina and promote collateral vessel development in patients with coronary artery disease. However, the mechanism whereby exercise exerts these beneficial effects is unclear. There has been increasing interest in the use of whole genome peripheral blood gene expression in a wide range of conditions to attempt to identify both novel mechanisms of disease and transcriptional biomarkers. This protocol describes a study in which we will assess the effect of a structured exercise programme on peripheral blood gene expression in patients with stable angina, and correlate this with changes in angina level, anxiety, depression, and exercise capacity. Methods/Design: Sixty patients with stable angina will be recruited and randomised 1: 1 to exercise training or conventional care. Patients randomised to exercise training will attend an exercise physiology laboratory up to three times weekly for supervised aerobic interval training sessions of one hour in total duration. Patients will undergo assessments of angina, anxiety, depression, and peripheral blood gene expression at baseline, after six and twelve weeks of training, and twelve weeks after formal exercise training ceases. Discussion: This study will provide comprehensive data on the effect of exercise training on peripheral blood gene expression in patients with angina. By correlating this with improvement in angina status we will identify candidate peripheral blood transcriptional markers predictive of improvements in angina level in response to exercise training

Overground walking speed changes when subjected to body weight support conditions for nonimpaired and post stroke individuals

<p>Abstract</p> <p>Background</p> <p>Previous research has shown that body weight support (BWS) has the potential to improve gait speed for individuals post-stroke. However, body weight support also reduces the optimal walking speed at which energy use is minimized over the gait cycle indicating that BWS should reduce walking speed capability.</p> <p>Methods</p> <p>Nonimpaired subjects and subjects post-stroke walked at a self-selected speed over a 15 m walkway. Body weight support (BWS) was provided to subjects at 0%, 10%, 20%, 30%, and 40% of the subject's weight while they walked overground using a robotic body weight support system. Gait speed, cadence, and average step length were calculated for each subject using recorded data on their time to walk 10 m and the number of steps taken.</p> <p>Results</p> <p>When subjected to greater levels of BWS, self-selected walking speed decreased for the nonimpaired subjects. However, subjects post-stroke showed an average increase of 17% in self-selected walking speed when subjected to some level of BWS compared to the 0% BWS condition. Most subjects showed this increase at the 10% BWS level. Gait speed increases corresponded to an increase in step length, but not cadence.</p> <p>Conclusions</p> <p>The BWS training environment results in decreased self-selected walking speed in nonimpaired individuals, however self-selected overground walking speed is facilitated when provided with a small percentage of body weight support for people post-stroke.</p

Modifiers of (CAG)(n) instability in Machado-Joseph disease (MJD/SCA3) transmissions: an association study with DNA replication, repair and recombination genes.

Twelve neurological disorders are caused by gene-specific CAG/CTG repeat expansions that are highly unstable upon transmission to offspring. This intergenerational repeat instability is clinically relevant since disease onset, progression and severity are associated with repeat size. Studies of model organisms revealed the involvement of some DNA replication and repair genes in the process of repeat instability, however, little is known about their role in patients. Here, we used an association study to search for genetic modifiers of (CAG)n instability in 137 parent-child transmissions in Machado-Joseph disease (MJD/SCA3). With the hypothesis that variants in genes involved in DNA replication, repair or recombination might alter the MJD CAG instability patterns, we screened 768 SNPs from 93 of these genes. We found a variant in ERCC6 (rs2228528) associated with an expansion bias of MJD alleles. When using a gene-gene interaction model, the allele combination G-A (rs4140804-rs2972388) of RPA3-CDK7 is also associated with MJD instability in a direction-dependent manner. Interestingly, the transcription-coupled repair factor ERCC6 (aka CSB), the single-strand binding protein RPA, and the CDK7 kinase part of the TFIIH transcription repair complex, have all been linked to transcription-coupled repair. This is the first study performed in patient samples to implicate specific modifiers of CAG instability in humans. In summary, we found variants in three transcription-coupled repair genes associated with the MJD mutation that points to distinct mechanisms of (CAG)n instability.This work was supported by the Canadian Institutes of Health Research; and the Levesque Chair for research in Neurogenetics [to G. A. R.]; and the Portuguese Foundation for Science and Technology [SFRH/BPD/77969/2011 to S.M]

Direct application of compound-specific radiocarbon analysis of leaf waxes to establish lacustrine sediment chronology

Author Posting. © Springer, 2007. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Journal of Paleolimnology 39 (2008): 43-60, doi:10.1007/s10933-007-9094-1.This study demonstrates use of compound-specific radiocarbon analysis (CSRA) for dating Holocene lacustrine sediments from carbonate-hosted Ordy Pond, Oahu, Hawaii. Long-chain odd-numbered normal alkanes (n-alkanes), biomarkers characteristic of terrestrial higher plants, were ubiquitous in Ordy Pond sediments. The δ13C of individual n-alkanes ranged from −29.9 to −25.5‰, within the expected range for n-alkanes synthesized by land plants using the C3 or C4 carbon fixation pathway. The 14C ages of n-alkanes determined by CSRA showed remarkably good agreement with 14C dates of rare plant macrofossils obtained from nearby sedimentary horizons. In general, CSRA of n-alkanes successfully refined the age-control of the sediments. The sum of n-alkanes in each sample produced 70–170 μg of carbon (C), however, greater age errors were confirmed for samples containing less than 80 μg of C. The 14C age of n-alkanes from one particular sedimentary horizon was 4,155 years older than the value expected from the refined age-control, resulting in an apparent and arguable age discrepancy. Several lines of evidence suggest that this particular sample was contaminated by introduction of 14C-free C during preparative capillary gas chromatography. This study simultaneously highlighted the promising potential of CSRA for paleo-applications and the risks of contamination associated with micro-scale 14C measurement of individual organic compounds.This project was funded by Petroleum Research Fund (PRF #40088-ACS) and in part by Sigma Xi, The Scientific Research Society (Grants in aid of research, 2003)

The impact of obesity on time spent with the provider and number of medications managed during office-based physician visits using a cross-sectional, national health survey

<p>Abstract</p> <p>Background</p> <p>Obesity is associated with morbidity, mortality, and increased health care costs. Few studies have examined the impact of obesity on outpatient office visits. The purpose of this study was to determine if outpatient visits by obese persons required more time with the provider and more prescription medication management compared to visits made by non-obese persons.</p> <p>Methods</p> <p>Obesity status was determined for 9,280 patient visits made by persons aged 18 years or older in the 2006 National Ambulatory Medical Care Survey. Multivariate analyses compared obese and non-obese visits, stratified by sex, for duration of the visit and the number of medications mentioned at the visit.</p> <p>Results</p> <p>Average duration of visit was higher among visits with patients determined to be obese. However, these differences were not considered significant after statistical testing. Visits made by obese female patients were significantly more likely to involve more than two prescription medications (OR 1.26, 95% CI 1.05 - 1.51) and visits made by obese male patients were significantly more likely to involve more than two prescription medications (OR 1.46, 95% CI 1.16 - 1.83) as compared to visits made by non-obese patients.</p> <p>Conclusion</p> <p>Time spent with the provider was found to be greater among visits with obese patients, but not significantly different from visits with non-obese patients. The number of medications for each visit was found to be significantly greater for visits where the patient was considered to be obese. Increased time for the visit and increased numbers of medication for each visit translate into increased costs. These findings document the impact of obesity on our health care system and have great implications on medical care cost and planning.</p

Comparison of Several Methods of Chromatographic Baseline Removal with a New Approach Based on Quantile Regression

The article is intended to introduce and discuss a new quantile regression method for baseline detrending of chromatographic signals. It is compared with current methods based on polynomial fitting, spline fitting, LOESS, and Whittaker smoother, each with thresholding and reweighting approach. For curve flexibility selection in existing algorithms, a new method based on skewness of the residuals is successfully applied. The computational efficiency of all approaches is also discussed. The newly introduced methods could be preferred to visible better performance and short computational time. The other algorithms behave in comparable way, and polynomial regression can be here preferred due to short computational time